Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001003.1 Hibiscus syriacus cultivar Beakdansim tig00002005_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60381
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1204 original size:19 final size:20
Alignment explanation
Indices: 1180--1231 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1170 AAACTTAAAT
*
1180 TCGCAATGCGAAAATG-AAA
1 TCGCAACGCGAAAATGAAAA
*
1199 TCGCAACGCAAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1219 TCGCAACGCGAAA
1 TCGCAACGCGAAA
1232 CTAAATTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1644 original size:22 final size:22
Alignment explanation
Indices: 1617--1667 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1607 GATGGAGATA
* * *
1617 GACGGATTTCGTCGGAGATGTG
1 GACGGATTACGTCAGAGATGGG
1639 GACGGATTACGTCAGAGATGGG
1 GACGGATTACGTCAGAGATGGG
1661 GACGGAT
1 GACGGAT
1668 GTCGCCGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.22
Consensus pattern (22 bp):
GACGGATTACGTCAGAGATGGG
Found at i:1813 original size:19 final size:19
Alignment explanation
Indices: 1789--1837 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1779 ATAAACGTGC
1789 TTTGACTTCTATGTTCG-AA
1 TTTGACTTCTATGTT-GAAA
* *
1808 TTTGACTTATGTGTTGTAAA
1 TTTGACTTCTATGTTG-AAA
1828 TTTGACTTCT
1 TTTGACTTCT
1838 GTGTAGCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 13 0.52
20 11 0.44
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.51
Consensus pattern (19 bp):
TTTGACTTCTATGTTGAAA
Found at i:1925 original size:20 final size:20
Alignment explanation
Indices: 1843--1926 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 20
1833 CTTCTGTGTA
*
1843 GCGATTTACAAATTCACGTT
1 GCGATTTACAAATTCGCGTT
1863 GCGATTTACAAATTCGCGTT
1 GCGATTTACAAATTCGCGTT
* ** * **
1883 ACGATTTGGAAAATCGCAAT
1 GCGATTTACAAATTCGCGTT
* *
1903 GCGATTCACATATTCGCGTT
1 GCGATTTACAAATTCGCGTT
1923 GCGA
1 GCGA
1927 ATTTGGAAAT
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (20 bp):
GCGATTTACAAATTCGCGTT
Found at i:1946 original size:40 final size:40
Alignment explanation
Indices: 1861--1971 Score: 102
Period size: 40 Copynumber: 2.8 Consensus size: 40
1851 CAAATTCACG
* *
1861 TTGCGATTTACAAATTCGCGTTACG-ATTTGGAAAATCGCA
1 TTGCGATTCAC-AATTCGCGTTGCGAATTTGGAAAATCGCA
* * *
1901 ATGCGATTCACATATTCGCGTTGCGAATTTGG-AAATTGGA
1 TTGCGATTCACA-ATTCGCGTTGCGAATTTGGAAAATCGCA
* *
1941 TTGCGAAATTGA-AGTTCGCGTTGCGAATTTG
1 TTGCG--ATTCACAATTCGCGTTGCGAATTTG
1972 AGATCGCGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
39 1 0.02
40 47 0.80
41 7 0.12
42 4 0.07
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (40 bp):
TTGCGATTCACAATTCGCGTTGCGAATTTGGAAAATCGCA
Found at i:1964 original size:20 final size:20
Alignment explanation
Indices: 1915--1989 Score: 84
Period size: 19 Copynumber: 3.8 Consensus size: 20
1905 GATTCACATA
*
1915 TTCGCGTTGCGAATTTGGAAA
1 TTCGCGTTGCGAATTT-GAAG
*
1936 TT-G-GATTGCGAAATTGAAG
1 TTCGCG-TTGCGAATTTGAAG
1955 TTCGCGTTGCGAATTTG-AG
1 TTCGCGTTGCGAATTTGAAG
*
1974 ATCGCGTTGCGAATTT
1 TTCGCGTTGCGAATTT
1990 ATTGGTCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 23 0.49
20 21 0.45
21 3 0.06
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.35
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTGAAG
Found at i:1978 original size:19 final size:19
Alignment explanation
Indices: 1916--1989 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
1906 ATTCACATAT
*
1916 TCGCGTTGCGAATTTGGAAA
1 TCGCGTTGCGAATTT-GAGA
* * *
1936 TTG-GATTGCGAAATTGAAGT
1 TCGCG-TTGCGAATTTG-AGA
1956 TCGCGTTGCGAATTTGAGA
1 TCGCGTTGCGAATTTGAGA
1975 TCGCGTTGCGAATTT
1 TCGCGTTGCGAATTT
1990 ATTGGTCATT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 19 0.43
20 24 0.55
21 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.34
Consensus pattern (19 bp):
TCGCGTTGCGAATTTGAGA
Found at i:6255 original size:3 final size:3
Alignment explanation
Indices: 6235--6275 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
6225 TTCTAACATG
*
6235 AAT AACT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6276 CAAAACAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:6276 original size:6 final size:6
Alignment explanation
Indices: 6235--6286 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
6225 TTCTAACATG
* * *
6235 AATAAC TAATAA- AATAAT AATAAT AATAAT AATAAC AATAAC AA-AAC
1 AATAAC -AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC
6282 AATAA
1 AATAA
6287 AAACTCTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
5 10 0.24
6 27 0.64
7 5 0.12
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (6 bp):
AATAAC
Found at i:12532 original size:23 final size:22
Alignment explanation
Indices: 12489--12532 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
12479 TCATACTTTA
*
12489 TAATATTTTCTTGCTTTATTAC
1 TAATATTTTCTAGCTTTATTAC
12511 TAATAGTTTTCTAG-TTTGATTA
1 TAATA-TTTTCTAGCTTT-ATTA
12533 GACTTCAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (22 bp):
TAATATTTTCTAGCTTTATTAC
Found at i:18576 original size:31 final size:32
Alignment explanation
Indices: 18540--18605 Score: 96
Period size: 35 Copynumber: 2.0 Consensus size: 32
18530 CAACAAGTCC
18540 AGTAAGGCCCTGAGCACACAGCAGAGGAGCCAGTA
1 AGTAAGGCCCTGAGCACACAGCAGAGGAGCC---A
*
18575 AGTAAGGCCCTGAGCACACAGCATAGGAGCC
1 AGTAAGGCCCTGAGCACACAGCAGAGGAGCC
18606 TCCAGGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.30, T:0.09
Consensus pattern (32 bp):
AGTAAGGCCCTGAGCACACAGCAGAGGAGCCA
Found at i:18731 original size:24 final size:24
Alignment explanation
Indices: 18695--18780 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 24
18685 CATAATTCAG
*
18695 GTCAGGTAACATATCAGAATCCAT
1 GTCAAGTAACATATCAGAATCCAT
* * * * *
18719 GTCAAGTAGCATATAAAAATTCAG
1 GTCAAGTAACATATCAGAATCCAT
* *
18743 GTCAGGTAACAGATCAGAATCCAT
1 GTCAAGTAACATATCAGAATCCAT
*
18767 GTCAAGTAGCATAT
1 GTCAAGTAACATAT
18781 AAAAATTCAG
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
GTCAAGTAACATATCAGAATCCAT
Found at i:18759 original size:48 final size:48
Alignment explanation
Indices: 18688--18806 Score: 229
Period size: 48 Copynumber: 2.5 Consensus size: 48
18678 ATTAAAACAT
*
18688 AATTCAGGTCAGGTAACATATCAGAATCCATGTCAAGTAGCATATAAA
1 AATTCAGGTCAGGTAACAGATCAGAATCCATGTCAAGTAGCATATAAA
18736 AATTCAGGTCAGGTAACAGATCAGAATCCATGTCAAGTAGCATATAAA
1 AATTCAGGTCAGGTAACAGATCAGAATCCATGTCAAGTAGCATATAAA
18784 AATTCAGGTCAGGTAACAGATCA
1 AATTCAGGTCAGGTAACAGATCA
18807 AATAACTATT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (48 bp):
AATTCAGGTCAGGTAACAGATCAGAATCCATGTCAAGTAGCATATAAA
Found at i:19519 original size:29 final size:29
Alignment explanation
Indices: 19492--19669 Score: 195
Period size: 29 Copynumber: 6.2 Consensus size: 29
19482 CTATTTTACA
* *
19492 AAAATAGCACCATTTTTAAAATAATTACC
1 AAAATAGCACCATTTTTAAATTAATTCCC
* * * *
19521 AAAATAACACCCTTTTTGAATTAATTTCC
1 AAAATAGCACCATTTTTAAATTAATTCCC
*
19550 AAAATAGCA-C-TTTTCAAATTAAATTCCC
1 AAAATAGCACCATTTTTAAATT-AATTCCC
19578 AAAATAG--CCATTTTTCAAATTAAATTCCC
1 AAAATAGCACCATTTTT-AAATT-AATTCCC
* *
19607 AAAATAGCACCCTTTTTGAATTAATTCCC
1 AAAATAGCACCATTTTTAAATTAATTCCC
*
19636 AAAATAGCACCCA-TTTTGAATTAATTCCC
1 AAAATAGCA-CCATTTTTAAATTAATTCCC
19665 AAAAT
1 AAAAT
19670 GTCACCCGAT
Statistics
Matches: 129, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
27 9 0.07
28 18 0.14
29 89 0.69
30 6 0.05
31 7 0.05
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAATAGCACCATTTTTAAATTAATTCCC
Found at i:19708 original size:18 final size:17
Alignment explanation
Indices: 19685--19755 Score: 115
Period size: 18 Copynumber: 4.1 Consensus size: 17
19675 CCGATCAACA
19685 GTCAACGGGTCGGGTCAG
1 GTCAACGGGTCGGGTC-G
*
19703 GTCAACGGGTCGAGTCGG
1 GTCAACGGGTCGGGTC-G
19721 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
19738 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
19755 G
1 G
19756 AACCGGTCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
17 19 0.38
18 31 0.62
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (17 bp):
GTCAACGGGTCGGGTCG
Found at i:25476 original size:2 final size:2
Alignment explanation
Indices: 25469--25519 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
25459 CATTCAGAGT
25469 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25511 TA TA TA TA T
1 TA TA TA TA T
25520 CTTACAATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26789 original size:29 final size:29
Alignment explanation
Indices: 26756--26818 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
26746 TATTTTATAG
26756 AAATAACACCCTTTTTAAAATAATTACCA
1 AAATAACACCCTTTTTAAAATAATTACCA
* * * * *
26785 AAATAGCACCCTTTTTGAATTAATTTCTA
1 AAATAACACCCTTTTTAAAATAATTACCA
26814 AAATA
1 AAATA
26819 GCACTTTTCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATAACACCCTTTTTAAAATAATTACCA
Found at i:26819 original size:29 final size:28
Alignment explanation
Indices: 26776--26931 Score: 163
Period size: 29 Copynumber: 5.5 Consensus size: 28
26766 CTTTTTAAAA
* *
26776 TAATTACCAAAATAGCACCCTTTTTGAAT
1 TAATTCCCAAAATAGCA-CCTTTTCGAAT
* *
26805 TAATTTCTAAAATAGCA-CTTTTCGAAT
1 TAATTCCCAAAATAGCACCTTTTCGAAT
* *
26832 TAAATTCCTAGAATAGCACCTTTTTCGAAT
1 T-AATTCCCAAAATAGCACC-TTTTCGAAT
*
26862 TAAATTCCCAAAATAGCA-CTTCTCGAAT
1 T-AATTCCCAAAATAGCACCTTTTCGAAT
* * *
26890 TAATTCCCAAAATATCACCCATTTCAAAT
1 TAATTCCCAAAATAGCA-CCTTTTCGAAT
26919 TAATTCCCAAAAT
1 TAATTCCCAAAAT
26932 GTTACCCGAT
Statistics
Matches: 110, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
27 25 0.23
28 23 0.21
29 37 0.34
30 25 0.23
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (28 bp):
TAATTCCCAAAATAGCACCTTTTCGAAT
Found at i:26847 original size:57 final size:56
Alignment explanation
Indices: 26776--26931 Score: 188
Period size: 57 Copynumber: 2.8 Consensus size: 56
26766 CTTTTTAAAA
* * * *
26776 TAATTACCAAAATAGCACCCTTTTTGAATTAATTTCTAAAATAGCACTTTTCGAAT
1 TAATTCCCAAAATAGCACCCTTTTTGAATTAATTCCCAAAATAGCACTTCTCGAAT
* *
26832 TAAATTCCTAGAATAGCA-CCTTTTTCGAATTAAATTCCCAAAATAGCACTTCTCGAAT
1 T-AATTCCCAAAATAGCACCCTTTTT-GAATT-AATTCCCAAAATAGCACTTCTCGAAT
* * **
26890 TAATTCCCAAAATATCACCCATTTCAAATTAATTCCCAAAAT
1 TAATTCCCAAAATAGCACCCTTTTTGAATTAATTCCCAAAAT
26932 GTTACCCGAT
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
56 20 0.24
57 35 0.42
58 29 0.35
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (56 bp):
TAATTCCCAAAATAGCACCCTTTTTGAATTAATTCCCAAAATAGCACTTCTCGAAT
Found at i:26969 original size:18 final size:18
Alignment explanation
Indices: 26946--27017 Score: 92
Period size: 18 Copynumber: 4.1 Consensus size: 18
26936 CCCGATCAAC
26946 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
* *
26964 GGTCAACGTGTCGAGTCG
1 GGTCAACGGGTCGGGTCG
*
26982 GGTCAACGGATCGGGTC-
1 GGTCAACGGGTCGGGTCG
* *
26999 GGTCAATGGGTCAGGTCG
1 GGTCAACGGGTCGGGTCG
27017 G
1 G
27018 AATCGGTCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
17 14 0.31
18 31 0.69
ACGTcount: A:0.15, C:0.21, G:0.44, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:28001 original size:86 final size:86
Alignment explanation
Indices: 27852--28023 Score: 290
Period size: 86 Copynumber: 2.0 Consensus size: 86
27842 TTTCTTTTTC
* **
27852 CACTTTAATTTTTTTAGTGTTGTGAATATTAAGGATGGCATAAGATGTAAAAGTATCTGAGACAT
1 CACTTTAATTTTTTTAGTGTTGTGAATATTAAGGATGACATAAGATGTAAAAGTATCCAAGACAT
*
27917 GCAAAAACTTCATGAACGCTA
66 GAAAAAACTTCATGAACGCTA
*
27938 CACTTTAATTTTTTTAGTGTTGTGAATATTCAGGATGACATAAGATGTAAAAGTATCCAAGACAT
1 CACTTTAATTTTTTTAGTGTTGTGAATATTAAGGATGACATAAGATGTAAAAGTATCCAAGACAT
*
28003 GAAAAAACTTCATGAATGCTA
66 GAAAAAACTTCATGAACGCTA
28024 TTAATGGTCT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (86 bp):
CACTTTAATTTTTTTAGTGTTGTGAATATTAAGGATGACATAAGATGTAAAAGTATCCAAGACAT
GAAAAAACTTCATGAACGCTA
Found at i:28685 original size:21 final size:21
Alignment explanation
Indices: 28661--28701 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28651 TCAAAGACAC
*
28661 TTACCAAGGTACTTCATCTAT
1 TTACCAAGGTAATTCATCTAT
*
28682 TTACCAATGTAATTCATCTA
1 TTACCAAGGTAATTCATCTA
28702 CTTCCACTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (21 bp):
TTACCAAGGTAATTCATCTAT
Found at i:31724 original size:13 final size:13
Alignment explanation
Indices: 31706--31732 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31696 TCTCTCCGGT
31706 TCTGTCTTTTTTC
1 TCTGTCTTTTTTC
31719 TCTGTCTTTTTTC
1 TCTGTCTTTTTTC
31732 T
1 T
31733 TTTTTTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.22, G:0.07, T:0.70
Consensus pattern (13 bp):
TCTGTCTTTTTTC
Found at i:32184 original size:3 final size:3
Alignment explanation
Indices: 32176--32261 Score: 104
Period size: 3 Copynumber: 29.0 Consensus size: 3
32166 TTAATATATT
* *
32176 TAA TAA TAA -AA -AA TAA TAA TAA TAA TAA TAA AAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
32222 TAT TAA TAA TGA TAA TAA TAA TTAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
32262 AATGGATAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
2 4 0.06
3 64 0.90
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:32269 original size:12 final size:11
Alignment explanation
Indices: 32178--32274 Score: 53
Period size: 12 Copynumber: 8.8 Consensus size: 11
32168 AATATATTTA
*
32178 ATAATAAAA-A
1 ATAATAAAATG
*
32188 ATAATAATAATA
1 ATAATAA-AATG
32200 ATAATAAAA--
1 ATAATAAAATG
* *
32209 ATAATGATAATA
1 ATAAT-AAAATG
*
32221 ATATTAATAATG
1 ATAATAA-AATG
32233 ATAATAATAAT-
1 ATAATAA-AATG
32244 -TAATAATAATG
1 ATAATAA-AATG
32255 ATAATAAAATGG
1 ATAATAAAAT-G
32267 ATAA-AAAA
1 ATAATAAAA
32275 AAATAGTATC
Statistics
Matches: 73, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
9 5 0.07
10 20 0.27
11 12 0.16
12 36 0.49
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:32753 original size:119 final size:119
Alignment explanation
Indices: 32509--33082 Score: 1007
Period size: 119 Copynumber: 4.9 Consensus size: 119
32499 GCTCTTGATG
*
32509 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
* * * * *
32570 TAC-CTGGTAATGTTGATCCATCAA-CTGATGAATTCAAGCAAAAGGTTGAACA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGATTGAACA
*
32622 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
32687 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGATTGAACA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGATTGAACA
32741 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
* *
32806 TTCTCTGGAAAAGATGATCCATCAATTTGATGAATTCAAGCAAAAGATTGAACA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGATTGAACA
*
32860 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTGCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
32925 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGATTGAACA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGATTGAACA
*
32979 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTGCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
33044 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAA
33083 ATCTTTGCTA
Statistics
Matches: 442, Mismatches: 13, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
113 37 0.08
116 21 0.05
117 3 0.01
118 19 0.04
119 362 0.82
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (119 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGATTGAACA
Found at i:33857 original size:50 final size:50
Alignment explanation
Indices: 33796--34448 Score: 1234
Period size: 50 Copynumber: 13.1 Consensus size: 50
33786 TCAATGATTG
* * *
33796 ATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
* *
33846 ATTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
*
33896 ATTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
33946 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
*
33996 ATTCTGTCTAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
34046 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
34096 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
34146 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
*
34196 ATTCTGTCTAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
34246 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
34296 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
34346 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
34396 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
34446 ATT
1 ATT
34449 AGTCTCTTTC
Statistics
Matches: 596, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 596 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (50 bp):
ATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
Found at i:46245 original size:17 final size:16
Alignment explanation
Indices: 46203--46255 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
46193 AAATACTTGC
46203 AAATAAAACATATAAAT
1 AAATAAAA-ATATAAAT
*
46220 ATTATAAAAATAATAAAT
1 A-AATAAAAAT-ATAAAT
46238 AAATAAAAAT-TAAA-
1 AAATAAAAATATAAAT
46252 AAAT
1 AAAT
46256 TTGAAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 4 0.12
15 4 0.12
17 11 0.34
18 13 0.41
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAAAATATAAAT
Found at i:48403 original size:3 final size:3
Alignment explanation
Indices: 48395--48489 Score: 120
Period size: 3 Copynumber: 32.0 Consensus size: 3
48385 TTAATATATT
* * *
48395 TAA TAA TAA -AA AAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
48442 TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48490 AATGGATAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:48497 original size:12 final size:11
Alignment explanation
Indices: 48400--48502 Score: 57
Period size: 12 Copynumber: 8.8 Consensus size: 11
48390 ATATTTAATA
* *
48400 ATAAAAAAATA
1 ATAATAAAATG
*
48411 ATAATAATAATA
1 ATAATAA-AATG
*
48423 ATAATAAAAATA
1 ATAAT-AAAATG
* *
48435 ATAATGATAATA
1 ATAAT-AAAATG
*
48447 ATATTAATAATG
1 ATAATAA-AATG
48459 ATAATAATAAT-
1 ATAATAA-AATG
48470 ATTAATAATAATG
1 A-TAATAA-AATG
48483 ATAATAAAATGG
1 ATAATAAAAT-G
48495 ATAA-AAAA
1 ATAATAAAA
48503 AAATAGTATC
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
11 15 0.19
12 61 0.77
13 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:51442 original size:2 final size:2
Alignment explanation
Indices: 51437--51471 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
51427 TATGTCTCTC
51437 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51472 CACTTTACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51989 original size:2 final size:2
Alignment explanation
Indices: 51982--52034 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
51972 CATGATCTGA
51982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
52024 AG AT AG AT AT A
1 AT AT AT AT AT A
52035 AATGAGAGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:56100 original size:20 final size:20
Alignment explanation
Indices: 56077--56144 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
56067 TTATGGGGGC
56077 ATCGATACTCTACCCTTGGT
1 ATCGATACTCTACCCTTGGT
*
56097 ATCGATACTCTACCCTTAGT
1 ATCGATACTCTACCCTTGGT
*
56117 ATCGATACCCTACCCTTGGT
1 ATCGATACTCTACCCTTGGT
56137 ATCGATAC
1 ATCGATAC
56145 CCCCTAAGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32
Consensus pattern (20 bp):
ATCGATACTCTACCCTTGGT
Found at i:58536 original size:21 final size:21
Alignment explanation
Indices: 58506--58567 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
58496 GACTACCGCA
* *
58506 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTTCTAATTCGCG
*
58527 TTGCGGTTTTTCTAATTCGCG
1 TTGCGATTTTTCTAATTCGCG
58548 TTGCGATTTTTCTAATTCGC
1 TTGCGATTTTTCTAATTCGC
58568 AATGCGAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (21 bp):
TTGCGATTTTTCTAATTCGCG
Found at i:58573 original size:21 final size:21
Alignment explanation
Indices: 58502--58574 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
58492 TTCTGACTAC
* *
58502 CGCATTGCGATTTTCCAAATT
1 CGCATTGCGATTTTTCTAATT
* *
58523 CGCGTTGCGGTTTTTCTAATT
1 CGCATTGCGATTTTTCTAATT
*
58544 CGCGTTGCGATTTTTCTAATT
1 CGCATTGCGATTTTTCTAATT
*
58565 CGCAATGCGA
1 CGCATTGCGA
58575 ATACGTAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.40
Consensus pattern (21 bp):
CGCATTGCGATTTTTCTAATT
Found at i:58589 original size:20 final size:20
Alignment explanation
Indices: 58564--58657 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
58554 TTTTTCTAAT
58564 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** *
58584 TCGCAACT-CGAATTTGGAAAA
1 TCGCAA-TGCGAA-TACGTAAA
*
58605 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
58625 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
58645 TCGCAATGCGAAT
1 TCGCAATGCGAAT
58658 CTGACTATCG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
20 48 0.76
21 15 0.24
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:58621 original size:41 final size:40
Alignment explanation
Indices: 58564--58657 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 40
58554 TTTTTCTAAT
**
58564 TCGCAATGCGAATACGTAAATCGCAACT-CGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAA-TGCGAA-TACGAAAA
* *
58605 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
58645 TCGCAATGCGAAT
1 TCGCAATGCGAAT
58658 CTGACTATCG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
40 18 0.38
41 29 0.62
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
Found at i:58667 original size:20 final size:20
Alignment explanation
Indices: 58657--58750 Score: 152
Period size: 20 Copynumber: 4.7 Consensus size: 20
58647 GCAATGCGAA
* * *
58657 TCTGACTATCGCAATGCGAA
1 TCTGACTATCGCAACGAGAT
58677 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
58697 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
58717 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
*
58737 TCTGACAATCGCAA
1 TCTGACTATCGCAA
58751 TACTGAATTT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
TCTGACTATCGCAACGAGAT
Found at i:59604 original size:24 final size:24
Alignment explanation
Indices: 59577--59630 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
59567 GTATTCAAAA
59577 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
59601 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
59625 TTTGAT
1 TTTGAT
59631 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Done.